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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="fasta2phytab" name="FASTA2PHYTAB" version="1.1">
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2 <description>Converts FASTA file with sequences from same gene family to PHYTAB format</description>
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3 <command interpreter="perl">
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4 #if $sp_opts.sp_opts_selector=="fasta"
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5 fasta2phytab.pl $infile 'from fasta' $partition $convert > $outfile
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6 #else
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7 fasta2phytab.pl $infile $sp_opts.species $partition $convert > $outfile
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8 #end if
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9 </command>
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10 <inputs>
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11 <param name="infile" type="data" format="fasta" label="Input File" help="fasta file to convert" />
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12 <conditional name="sp_opts">
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13 <param name="sp_opts_selector" type="select" label="Species Name Source">
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14 <option value="fasta" selected="True">Take from fasta header</option>
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15 <option value="user">user input</option>
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16 </param>
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17 <when value="fasta">
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18 <param name="species" type="hidden" value="from fasta" label="Species" help="" />
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19 </when>
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20 <when value="user">
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21 <param name="species" type="text" format="tabular" label="Input name of species" help="" />
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22 </when>
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23 </conditional>
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24 <param name="partition" type="text" format="tabular" label="Name of partition" help="" />
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25 <param name="convert" type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Replace pipes with underscores' />
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26 </inputs>
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27 <outputs>
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28 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}: Out file" />
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29 </outputs>
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30 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 **What it does**
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32
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33 FASTA2PHYTAB takes an input FASTA file with sequences from the same gene family, and adds species name - either from the fasta header or from a single text entry - and
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34 partition (gene family) name that will apply for all sequences. The output is a PHYTAB tabular format file.
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35
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36 ------
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37
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38 **Inputs**
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39
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40 A FASTA file with all sequences from the same gene family.
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41
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42 ------
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43
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44 **Outputs**
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45
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46 PHYTAB file format: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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47
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48 -------
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49
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50 **Additional Information**
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51
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52 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
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53 osiris_phylogenetics site at bitbucket.org
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54
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55 ------
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56
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57 **Citations**
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58
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59 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a
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60 publication, please consider citing the following.
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61
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62 Current Osiris Citation is here
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63
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64 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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65 </help>
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66 </tool>